[English] 日本語
Yorodumi- PDB-6tb7: Crystal structure of the ADP-binding domain of the NAD+ riboswitc... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6tb7 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the ADP-binding domain of the NAD+ riboswitch with Adenosine monophosphate (AMP) | ||||||
Components | RNA | ||||||
Keywords | RNA / RNA structure / tRNA-mimicking / X-ray crystallography | ||||||
Function / homology | ADENOSINE MONOPHOSPHATE / BROMIDE ION / : / RNA / RNA (> 10) Function and homology information | ||||||
Biological species | Candidatus Koribacter versatilis Ellin345 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.53 Å | ||||||
Authors | Huang, L. / Lilley, D.M.J. | ||||||
Funding support | United Kingdom, 1items
| ||||||
Citation | Journal: Rna / Year: 2020 Title: Structure and ligand binding of the ADP-binding domain of the NAD + riboswitch. Authors: Huang, L. / Wang, J. / Lilley, D.M.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6tb7.cif.gz | 74.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6tb7.ent.gz | 53.6 KB | Display | PDB format |
PDBx/mmJSON format | 6tb7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tb7_validation.pdf.gz | 694.1 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6tb7_full_validation.pdf.gz | 695 KB | Display | |
Data in XML | 6tb7_validation.xml.gz | 4.5 KB | Display | |
Data in CIF | 6tb7_validation.cif.gz | 5.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/6tb7 ftp://data.pdbj.org/pub/pdb/validation_reports/tb/6tb7 | HTTPS FTP |
-Related structure data
Related structure data | 6tf0C 6tf1C 6tf2C 6tf3C 6tfeC 6tffC 6tfgC 6tfhC C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
|
-Components
-RNA chain , 1 types, 1 molecules A
#1: RNA chain | Mass: 16785.062 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Candidatus Koribacter versatilis Ellin345 (bacteria) References: GenBank: 94549081 |
---|
-Non-polymers , 5 types, 30 molecules
#2: Chemical | ChemComp-AMP / | ||||||
---|---|---|---|---|---|---|---|
#3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-NA / #5: Chemical | ChemComp-BR / | #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 5.02 Å3/Da / Density % sol: 75.5 % |
---|---|
Crystal grow | Temperature: 280 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 0.2 M Potassium Chloride, 0.1 M Mg Acetate, 0.05 M Sodium Cacodylate pH 7.0, 10% w/v Polyethylene Glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9186 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 20, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9186 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→47.6 Å / Num. obs: 20563 / % possible obs: 98.36 % / Redundancy: 6.2 % / Biso Wilson estimate: 71.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Net I/σ(I): 20.06 |
Reflection shell | Resolution: 2.53→2.57 Å / Rmerge(I) obs: 1.8 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 540 / CC1/2: 0.48 / Rpim(I) all: 0.99 / % possible all: 97.7 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SAD / Resolution: 2.53→47.59 Å / SU ML: 0.5921 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 37.4525
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 84.19 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.53→47.59 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|